From 36a7657de9cef2333113f5389fba22b905a03b69 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Thu, 31 Jul 2014 14:21:23 +0200
Subject: [PATCH] Fixed bug in transposition description.
---
mutalyzer/describe.py | 18 +++++++++---------
mutalyzer/models.py | 4 ++++
2 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 194179fe..38b82924 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -217,8 +217,8 @@ class SeqList(list):
return representation
#__str__
- def __nonzero__(self):
- return bool(self[0])
+ #def __nonzero__(self):
+ # return bool(len(self))
#SeqList
class RawVar(models.RawVar):
@@ -623,8 +623,8 @@ def describe(s1, s2, dna=True):
for variant in extractor.extract(unicode(s1), len(s1), unicode(s2), len(s2),
0):
- #print variant.type, variant.reference_start, variant.reference_end, variant.sample_start, variant.sample_end
- #print variant.type & extractor.TRANSPOSITION_OPEN, variant.type & extractor.TRANSPOSITION_CLOSE
+ #print variant.type, variant.reference_start, variant.reference_end, variant.sample_start, variant.sample_end, variant.transposition_start, variant.transposition_end
+ #print variant.type & extractor.TRANSPOSITION_OPEN, variant.type & extractor.TRANSPOSITION_CLOSE
if variant.type & extractor.TRANSPOSITION_OPEN:
if not in_transposition:
@@ -635,18 +635,18 @@ def describe(s1, s2, dna=True):
if in_transposition:
if variant.type & extractor.IDENTITY:
seq_list.append(Seq(#reference=s1,
- start=variant.sample_start + 1, end=variant.sample_end,
- reverse=False))
+ start=variant.transposition_start + 1,
+ end=variant.transposition_end, reverse=False))
elif variant.type & extractor.REVERSE_COMPLEMENT:
seq_list.append(Seq(#reference=s1,
- start=variant.sample_start + 1, end=variant.sample_end,
- reverse=True))
+ start=variant.transposition_start + 1,
+ end=variant.transposition_end, reverse=True))
else:
seq_list.append(Seq(
sequence=s2[variant.sample_start:variant.sample_end]))
#if
elif not (variant.type & extractor.IDENTITY):
- description.append(var_to_rawvar(s1, s2, variant, dna=dna))
+ description.append(var_to_rawvar(s1, s2, variant, dna=dna))
if variant.type & extractor.TRANSPOSITION_CLOSE:
in_transposition -= 1
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index 50202aab..10012a83 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -114,6 +114,10 @@ class RawVar(ComplexModel):
sample_start_offset = Mandatory.Integer
sample_end = Mandatory.Integer
sample_end_offset = Mandatory.Integer
+ transposition_start = Mandatory.Integer
+ transposition_start_offset = Mandatory.Integer
+ transposition_end = Mandatory.Integer
+ transposition_end_offset = Mandatory.Integer
type = Mandatory.Unicode
deleted = Mandatory.Unicode
inserted = Mandatory.Unicode
--
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